PTK6 (BRK) is an oncogenic non-receptor tyrosine kinase that functions downstream of ERBB2 (HER2) (Xiang et al. 2008, Peng et al. 2015) and other receptor tyrosine kinases, such as EGFR (Kamalati et al. 1996) and MET (Castro and Lange 2010). Since ERBB2 forms heterodimers with EGFR and since MET can heterodimerize with both ERBB2 and EGFR (Tanizaki et al. 2011), it is not clear if MET and EGFR activate PTK6 directly or act through ERBB2. Levels of PTK6 increase under hypoxic conditions (Regan Anderson et al. 2013, Pires et al. 2014). The kinase activity of PTK6 is negatively regulated by PTPN1 phosphatase (Fan et al. 2013) and SRMS kinase (Fan et al. 2015), as well as the STAT3 target SOCS3 (Gao et al. 2012).
PTK6 activates STAT3-mediated transcription (Ikeda et al. 2009, Ikeda et al. 2010) and may also activate STAT5-mediated transcription (Ikeda et al. 2011). PTK6 promotes cell motility and migration by regulating the activity of RHO GTPases RAC1 (Chen et al. 2004) and RHOA (Shen et al. 2008), and possibly by affecting motility-related kinesins (Lukong and Richard 2008). PTK6 crosstalks with AKT1 (Zhang et al. 2005, Zheng et al. 2010) and RAS signaling cascades (Shen et al. 2008, Ono et al. 2014) and may be involved in MAPK7 (ERK5) activation (Ostrander et al. 2007, Zheng et al. 2012). PTK6 enhances EGFR signaling by inhibiting EGFR down-regulation (Kang et al. 2010, Li et al. 2012, Kang and Lee 2013). PTK6 may also enhance signaling by IGF1R (Fan et al. 2013) and ERBB3 (Kamalati et al. 2000).<p>PTK6 promotes cell cycle progression by phosphorylating and inactivating CDK inhibitor CDKN1B (p27) (Patel et al. 2015).<p>PTK6 activity is upregulated in osteopontin (OPN or SPP1)-mediated signaling, leading to increased VEGF expression via PTK6/NF-kappaB/ATF4 signaling path. PTK6 may therefore play a role in VEGF-dependent tumor angiogenesis (Chakraborty et al. 2008).<p>PTK6 binds and phosphorylates several nuclear RNA-binding proteins, including SAM68 family members (KHDRSB1, KHDRSB2 and KHDRSB3) (Derry et al. 2000, Haegebarth et al. 2004, Lukong et al. 2005) and SFPQ (PSF) (Lukong et al. 2009). The biological role of PTK6 in RNA processing is not known.<p>For a review of PTK6 function, please refer to Goel and Lukong 2015.
View original pathway at Reactome.</div>
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Wiejak J, Dunlop J, Gao S, Borland G, Yarwood SJ.; ''Extracellular signal-regulated kinase mitogen-activated protein kinase-dependent SOCS-3 gene induction requires c-Jun, signal transducer and activator of transcription 3, and specificity protein 3 transcription factors.''; PubMedEurope PMCScholia
Brill S, Li S, Lyman CW, Church DM, Wasmuth JJ, Weissbach L, Bernards A, Snijders AJ.; ''The Ras GTPase-activating-protein-related human protein IQGAP2 harbors a potential actin binding domain and interacts with calmodulin and Rho family GTPases.''; PubMedEurope PMCScholia
Semenza GL.; ''Hydroxylation of HIF-1: oxygen sensing at the molecular level.''; PubMedEurope PMCScholia
Ahmadian MR, Kiel C, Stege P, Scheffzek K.; ''Structural fingerprints of the Ras-GTPase activating proteins neurofibromin and p120GAP.''; PubMedEurope PMCScholia
Bassi ZI, Audusseau M, Riparbelli MG, Callaini G, D'Avino PP.; ''Citron kinase controls a molecular network required for midbody formation in cytokinesis.''; PubMedEurope PMCScholia
Hannon GJ, Beach D.; ''p15INK4B is a potential effector of TGF-beta-induced cell cycle arrest.''; PubMedEurope PMCScholia
Wellbrock C, Karasarides M, Marais R.; ''The RAF proteins take centre stage.''; PubMedEurope PMCScholia
Brown MD, Sacks DB.; ''Protein scaffolds in MAP kinase signalling.''; PubMedEurope PMCScholia
Collazos A, Michael N, Whelan RD, Kelly G, Mellor H, Pang LC, Totty N, Parker PJ.; ''Site recognition and substrate screens for PKN family proteins.''; PubMedEurope PMCScholia
Wang S, Watanabe T, Noritake J, Fukata M, Yoshimura T, Itoh N, Harada T, Nakagawa M, Matsuura Y, Arimura N, Kaibuchi K.; ''IQGAP3, a novel effector of Rac1 and Cdc42, regulates neurite outgrowth.''; PubMedEurope PMCScholia
Lammers M, Rose R, Scrima A, Wittinghofer A.; ''The regulation of mDia1 by autoinhibition and its release by Rho*GTP.''; PubMedEurope PMCScholia
Vega FM, Fruhwirth G, Ng T, Ridley AJ.; ''RhoA and RhoC have distinct roles in migration and invasion by acting through different targets.''; PubMedEurope PMCScholia
Scheffzek K, Ahmadian MR, Kabsch W, Wiesmüller L, Lautwein A, Schmitz F, Wittinghofer A.; ''The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants.''; PubMedEurope PMCScholia
Fan G, Lin G, Lucito R, Tonks NK.; ''Protein-tyrosine phosphatase 1B antagonized signaling by insulin-like growth factor-1 receptor and kinase BRK/PTK6 in ovarian cancer cells.''; PubMedEurope PMCScholia
Ikeda O, Sekine Y, Mizushima A, Nakasuji M, Miyasaka Y, Yamamoto C, Muromoto R, Nanbo A, Oritani K, Yoshimura A, Matsuda T.; ''Interactions of STAP-2 with Brk and STAT3 participate in cell growth of human breast cancer cells.''; PubMedEurope PMCScholia
Schlessinger J.; ''Ligand-induced, receptor-mediated dimerization and activation of EGF receptor.''; PubMedEurope PMCScholia
Zhang W, Benson DL.; ''Targeting and clustering citron to synapses.''; PubMedEurope PMCScholia
Yang J, Huang J, Dasgupta M, Sears N, Miyagi M, Wang B, Chance MR, Chen X, Du Y, Wang Y, An L, Wang Q, Lu T, Zhang X, Wang Z, Stark GR.; ''Reversible methylation of promoter-bound STAT3 by histone-modifying enzymes.''; PubMedEurope PMCScholia
Bagchi S, Weinmann R, Raychaudhuri P.; ''The retinoblastoma protein copurifies with E2F-I, an E1A-regulated inhibitor of the transcription factor E2F.''; PubMedEurope PMCScholia
Szczepanowska J.; ''Involvement of Rac/Cdc42/PAK pathway in cytoskeletal rearrangements.''; PubMedEurope PMCScholia
Guan KL, Jenkins CW, Li Y, O'Keefe CL, Noh S, Wu X, Zariwala M, Matera AG, Xiong Y.; ''Isolation and characterization of p19INK4d, a p16-related inhibitor specific to CDK6 and CDK4.''; PubMedEurope PMCScholia
Oxygen plays a central role in the functioning of human cells: it is both essential for normal metabolism and toxic. Here we have annotated one aspect of cellular responses to oxygen, the role of hypoxia-inducible factor in regulating cellular transcriptional responses to changes in oxygen availability.
In the presence of oxygen members of the transcription factor family HIF-alpha, comprising HIF1A, HIF2A (EPAS1), and HIF3A, are hydroxylated on proline residues by PHD1 (EGLN2), PHD2 (EGLN1), and PHD3 (EGLN3) and on asparagine residues by HIF1AN (FIH) (reviewed in Pouyssegur et al. 2006, Semenza 2007, Kaelin and Ratcliffe 2008, Nizet and Johnson 2009, Brahimi-Horn and Pouyssegur 2009, Majmundar et al. 2010, Loenarz and Schofield 2011). Both types of reaction require molecular oxygen as a substrate and it is probable that at least some HIF-alpha molecules carry both hydroxylated asparagine and hydroxylated proline (Tian et al. 2011). Hydroxylated asparagine interferes with the ability of HIF-alpha to interact with p300 and CBP while hydroxylated proline facilitates the interaction of HIF-alpha with the E3 ubiquitin ligase VHL, causing ubiquitination and proteolysis of HIF-alpha. Hypoxia inhibits both types of hydroxylation, resulting in the stabilization of HIF-alpha, which then enters the nucleus, binds HIF-beta, and recruits p300 and CBP to activate target genes such as EPO and VEGF.
Mitotic G1-G1/S phase involves G1 phase of the mitotic interphase and G1/S transition, when a cell commits to DNA replication and divison genetic and cellular material to two daughter cells.
During early G1, cells can enter a quiescent G0 state. In quiescent cells, the evolutionarily conserved DREAM complex, consisting of the pocket protein family member p130 (RBL2), bound to E2F4 or E2F5, and the MuvB complex, represses transcription of cell cycle genes (reviewed by Sadasivam and DeCaprio 2013).
During early G1 phase in actively cycling cells, transcription of cell cycle genes is repressed by another pocket protein family member, p107 (RBL1), which forms a complex with E2F4 (Ferreira et al. 1998, Cobrinik 2005). RB1 tumor suppressor, the product of the retinoblastoma susceptibility gene, is the third member of the pocket protein family. RB1 binds to E2F transcription factors E2F1, E2F2 and E2F3 and inhibits their transcriptional activity, resulting in prevention of G1/S transition (Chellappan et al. 1991, Bagchi et al. 1991, Chittenden et al. 1991, Lees et al. 1993, Hiebert 1993, Wu et al. 2001). Once RB1 is phosphorylated on serine residue S795 by Cyclin D:CDK4/6 complexes, it can no longer associate with and inhibit E2F1-3. Thus, CDK4/6-mediated phosphorylation of RB1 leads to transcriptional activation of E2F1-3 target genes needed for the S phase of the cell cycle (Connell-Crowley et al. 1997). CDK2, in complex with cyclin E, contributes to RB1 inactivation and also activates proteins needed for the initiation of DNA replication (Zhang 2007). Expression of D type cyclins is regulated by extracellular mitogens (Cheng et al. 1998, Depoortere et al. 1998). Catalytic activities of CDK4/6 and CDK2 are controlled by CDK inhibitors of the INK4 family (Serrano et al. 1993, Hannon and Beach 1994, Guan et al. 1994, Guan et al. 1996, Parry et al. 1995) and the Cip/Kip family, respectively.
Signaling by AKT is one of the key outcomes of receptor tyrosine kinase (RTK) activation. AKT is activated by the cellular second messenger PIP3, a phospholipid that is generated by PI3K. In ustimulated cells, PI3K class IA enzymes reside in the cytosol as inactive heterodimers composed of p85 regulatory subunit and p110 catalytic subunit. In this complex, p85 stabilizes p110 while inhibiting its catalytic activity. Upon binding of extracellular ligands to RTKs, receptors dimerize and undergo autophosphorylation. The regulatory subunit of PI3K, p85, is recruited to phosphorylated cytosolic RTK domains either directly or indirectly, through adaptor proteins, leading to a conformational change in the PI3K IA heterodimer that relieves inhibition of the p110 catalytic subunit. Activated PI3K IA phosphorylates PIP2, converting it to PIP3; this reaction is negatively regulated by PTEN phosphatase. PIP3 recruits AKT to the plasma membrane, allowing TORC2 to phosphorylate a conserved serine residue of AKT. Phosphorylation of this serine induces a conformation change in AKT, exposing a conserved threonine residue that is then phosphorylated by PDPK1 (PDK1). Phosphorylation of both the threonine and the serine residue is required to fully activate AKT. The active AKT then dissociates from PIP3 and phosphorylates a number of cytosolic and nuclear proteins that play important roles in cell survival and metabolism. For a recent review of AKT signaling, please refer to Manning and Cantley, 2007.
The RAS-RAF-MEK-ERK pathway regulates processes such as proliferation, differentiation, survival, senescence and cell motility in response to growth factors, hormones and cytokines, among others. Binding of these stimuli to receptors in the plasma membrane promotes the GEF-mediated activation of RAS at the plasma membrane and initiates the three-tiered kinase cascade of the conventional MAPK cascades. GTP-bound RAS recruits RAF (the MAPK kinase kinase), and promotes its dimerization and activation (reviewed in Cseh et al, 2014; Roskoski, 2010; McKay and Morrison, 2007; Wellbrock et al, 2004). Activated RAF phosphorylates the MAPK kinase proteins MEK1 and MEK2 (also known as MAP2K1 and MAP2K2), which in turn phophorylate the proline-directed kinases ERK1 and 2 (also known as MAPK3 and MAPK1) (reviewed in Roskoski, 2012a, b; Kryiakis and Avruch, 2012). Activated ERK proteins may undergo dimerization and have identified targets in both the nucleus and the cytosol; consistent with this, a proportion of activated ERK protein relocalizes to the nucleus in response to stimuli (reviewed in Roskoski 2012b; Turjanski et al, 2007; Plotnikov et al, 2010; Cargnello et al, 2011). Although initially seen as a linear cascade originating at the plasma membrane and culminating in the nucleus, the RAS/RAF MAPK cascade is now also known to be activated from various intracellular location. Temporal and spatial specificity of the cascade is achieved in part through the interaction of pathway components with numerous scaffolding proteins (reviewed in McKay and Morrison, 2007; Brown and Sacks, 2009). The importance of the RAS/RAF MAPK cascade is highlighted by the fact that components of this pathway are mutated with high frequency in a large number of human cancers. Activating mutations in RAS are found in approximately one third of human cancers, while ~8% of tumors express an activated form of BRAF (Roberts and Der, 2007; Davies et al, 2002; Cantwell-Dorris et al, 2011).
Formins are a family of proteins with 15 members in mammals, organized into 8 subfamilies. Formins are involved in the regulation of actin cytoskeleton. Many but not all formin family members are activated by RHO GTPases. Formins that serve as effectors of RHO GTPases belong to different formin subfamilies but they all share a structural similarity to Drosophila protein diaphanous and are hence named diaphanous-related formins (DRFs).
DRFs activated by RHO GTPases contain a GTPase binding domain (GBD) at their N-terminus, followed by formin homology domains 3, 1, and 2 (FH3, FH1, FH2) and a diaphanous autoregulatory domain (DAD) at the C-terminus. Most DRFs contain a dimerization domain (DD) and a coiled-coil region (CC) in between FH3 and FH1 domains (reviewed by Kuhn and Geyer 2014). RHO GTPase-activated DRFs are autoinhibited through the interaction between FH3 and DAD which is disrupted upon binding to an active RHO GTPase (Li and Higgs 2003, Lammers et al. 2005, Nezami et al. 2006). Since formins dimerize, it is not clear whether the FH3-DAD interaction is intra- or intermolecular. FH2 domain is responsible for binding to the F-actin and contributes to the formation of head-to-tail formin dimers (Xu et al. 2004). The proline-rich FH1 domain interacts with the actin-binding proteins profilins, thereby facilitating actin recruitment to formins and accelerating actin polymerization (Romero et al. 2004, Kovar et al. 2006).
Different formins are activated by different RHO GTPases in different cell contexts. FMNL1 (formin-like protein 1) is activated by binding to the RAC1:GTP and is involved in the formation of lamellipodia in macrophages (Yayoshi-Yamamoto et al. 2000) and is involved in the regulation of the Golgi complex structure (Colon-Franco et al. 2011). Activation of FMNL1 by CDC42:GTP contributes to the formation of the phagocytic cup (Seth et al. 2006). Activation of FMNL2 (formin-like protein 2) and FMNL3 (formin-like protein 3) by RHOC:GTP is involved in cancer cell motility and invasiveness (Kitzing et al. 2010, Vega et al. 2011). DIAPH1, activated by RHOA:GTP, promotes elongation of actin filaments and activation of SRF-mediated transcription which is inhibited by unpolymerized actin (Miralles et al. 2003). RHOF-mediated activation of DIAPH1 is implicated in formation of stress fibers (Fan et al. 2010). Activation of DIAPH1 and DIAPH3 by RHOB:GTP leads to actin coat formation around endosomes and regulates endosome motility and trafficking (Fernandez-Borja et al. 2005, Wallar et al. 2007). Endosome trafficking is also regulated by DIAPH2 transcription isoform 3 (DIAPH2-3) which, upon activation by RHOD:GTP, recruits SRC kinase to endosomes (Tominaga et al. 2000, Gasman et al. 2003). DIAPH2 transcription isoform 2 (DIAPH2-2) is involved in mitosis where, upon being activated by CDC42:GTP, it facilitates the capture of astral microtubules by kinetochores (Yasuda et al. 2004, Cheng et al. 2011). DIAPH2 is implicated in ovarian maintenance and premature ovarian failure (Bione et al. 1998). DAAM1, activated by RHOA:GTP, is involved in linking WNT signaling to cytoskeleton reorganization (Habas et al. 2001).
WASP and WAVE proteins belong to the Wiskott-Aldrich Syndrome protein family, with recessive mutations in the founding member WASP being responsible for the X-linked recessive immunodeficieny known as the Wiskott-Aldrich Syndrome. WASP proteins include WASP and WASL (N-WASP). WAVE proteins include WASF1 (WAVE1), WASF2 (WAVE2) and WASF3 (WAVE3). WASPs and WAVEs contain a VCA domain (consisting of WH2 and CA subdomains) at the C-terminus, responsible for binding to G-actin (WH2 subdomain) and the actin-associated ARP2/3 complex (CA subdomain). WASPs contain a WH1 (WASP homology 1) domain at the N-terminus, responsible for binding to WIPs (WASP-interacting proteins). A RHO GTPase binding domain (GBD) is located in the N-terminal half of WASPs and C-terminally located in WAVEs. RHO GTPases activate WASPs by disrupting the autoinhibitory interaction between the GBD and VCA domains, which allows WASPs to bind actin and the ARP2/3 complex and act as nucleation promoting factors in actin polymerization. WAVEs have the WAVE/SCAR homology domain (WHD/SHD) at the N-terminus, which binds ABI, NCKAP1, CYFIP2 and BRK1 to form the WAVE regulatory complex (WRC). Binding of the RAC1:GTP to the GBD of WAVEs most likely induces a conformational change in the WRC that allows activating phosphorylation of WAVEs by ABL1, thus enabling them to function as nucleation promoting factors in actin polymerization through binding G-actin and the ARP2/3 complex (Reviewed by Lane et al. 2014).
Citron kinase (CIT) or citron RHO-interacting kinase (CRIK) shares similarities with ROCK kinases. Like ROCK, it consists of a serine/threonine kinase domain, a coiled-coil region, a RHO-binding domain, a cysteine rich region and a plekstrin homology (PH) domain, but additionally features a proline-rich region and a PDZ-binding domain. A shorter splicing isoform of CIT, citron-N, is specifically expressed in the nervous system and lacks the kinase domain. Citron-N is a component of the post-synaptic density, where it binds to the PDZ domains of the scaffolding protein PDS-95/SAP90 (Zhang et al. 2006).
While the binding of CIT to RHO GTPases RHOA, RHOB, RHOC and RAC1 is well established (Madaule et al. 1995), the mechanism of CIT activation by GTP-bound RHO GTPases has not been elucidated. There are indications that CIT may be activated through autophosphorylation in the presence of active forms of RHO GTPases (Di Cunto et al. 1998). CIT appears to phosphorylate the myosin regulatory light chain (MRLC), the only substrate identified to date, on the same residues that are phosphorylated by ROCKs, but it has not been established yet how this relates to activation by RHO GTPases (Yamashiro et al. 2003). CIT and RHOA are implicated to act together in Golgi apparatus organization through regulation of the actin cytoskeleton (Camera et al. 2003). CIT is also involved in the regulation of cytokinesis through its interaction with KIF14 (Gruneberg et al. 2006, Bassi et al. 2013, Watanabe et al. 2013) and p27(Kip1) (Serres et al. 2012).
IQGAPs constitute a family of scaffolding proteins characterized by a calponin homology (CH) domain, a polyproline binding region (WW domain), a tandem of four IQ (isoleucine and glutamine-rich) repeats and a RAS GTPase-activating protein-related domain (GRD). Three IQGAPs have been identified in human, IQGAP1, IQGAP2 and IQGAP3. The best characterized is IQGAP1 and over 90 proteins have been reported to bind to it. IQGAPs integrate multiple signaling pathways and coordinate a large variety of cellular activities (White et al. 2012). IQGAP proteins IQGAP1, IQGAP2 and IQGAP3, bind activated RHO GTPases RAC1 and CDC42 via their GRD and stabilize them in their GTP-bound state (Kuroda et al. 1996, Swart-Mataraza et al. 2002, Wang et al. 2007). IQGAPs bind F-actin filaments via the CH domain and modulate cell shape and motility through regulation of G-actin/F-actin equilibrium (Brill et al. 1996, Fukata et al. 1997, Bashour et al. 1997, Wang et al. 2007, Pelikan-Conchaudron et al. 2011). Binding of IQGAPs to F-actin is inhibited by calmodulin binding to the IQ repeats (Bashour et al. 1997, Pelikan-Conchaudron et al. 2011). Based on IQGAP1 studies, IQGAPs presumably function as homodimers (Bashour et al. 1997).
IQGAP1 is involved in the regulation of adherens junctions through its interaction with E-cadherin (CDH1) and catenins (CTTNB1 and CTTNA1) (Kuroda et al. 1998, Hage et al. 2009). IQGAP1 contributes to cell polarity and lamellipodia formation through its interaction with microtubules (Fukata et al. 2002, Suzuki and Takahashi 2008).
GTP-bound active forms of RHO GTPases RHOA, RHOG, RAC1 and CDC42 bind kinectin (KTN1), a protein inserted in endoplasmic reticulum membranes that interacts with the cargo-binding site of kinesin and activates its microtubule-stimulated ATPase activity required for vesicle motility (Vignal et al. 2001, Hotta et al. 1996). The effect of RHOG activity on cellular morphology, exhibited in the formation of microtubule-dependent cellular protrusions, depends both on RHOG interaction with KTN1, as well as on the kinesin activity (Vignal et al. 2001). RHOG and KTN1 also cooperate in microtubule-dependent lysosomal transport (Vignal et al. 2001). The precise mechanism of kinectin-mediated Rho GTPase signaling cascade needs further elucidation, and only the first two steps, KTN1-activated RHO GTPase binding, and KTN1-kinesin-1 binding are annotated here.
The PAKs (p21-activated kinases) are a family of serine/threonine kinases mainly implicated in cytoskeletal rearrangements. All PAKs share a conserved catalytic domain located at the carboxyl terminus and a highly conserved motif in the amino terminus known as p21-binding domain (PBD) or Cdc42/Rac interactive binding (CRIB) domain. There are six mammalian PAKs that can be divided into two classes: class I (or conventional) PAKs (PAK1-3) and class II PAKs (PAK4-6). Conventional PAKs are important regulators of cytoskeletal dynamics and cell motility and are additionally implicated in transcription through MAPK (mitogen-activated protein kinase) cascades, death and survival signaling and cell cycle progression (Chan and Manser 2012).
PAK1, PAK2 and PAK3 are direct effectors of RAC1 and CDC42 GTPases. RAC1 and CDC42 bind to the CRIB domain. This binding induces a conformational change that disrupts inactive PAK homodimers and relieves autoinhibition of the catalytic carboxyl terminal domain (Manser et al. 1994, Manser et al. 1995, Zhang et al. 1998, Lei et al. 2000, Parrini et al. 2002; reviewed by Daniels and Bokoch 1999, Szczepanowska 2009). Autophosphorylation of a conserved threonine residue in the catalytic domain of PAKs (T423 in PAK1, T402 in PAK2 and T436 in PAK3) is necessary for the kinase activity of PAK1, PAK2 and PAK3. Autophosphorylation of PAK1 serine residue S144, PAK2 serine residue S141, and PAK3 serine residue S154 disrupts association of PAKs with RAC1 or CDC42 and enhances kinase activity (Lei et al. 2000, Chong et al. 2001, Parrini et al. 2002, Jung and Traugh 2005, Wang et al. 2011). LIMK1 is one of the downstream targets of PAK1 and is activated through PAK1-mediated phosphorylation of the threonine residue T508 within its activation loop (Edwards et al. 1999). Further targets are the myosin regulatory light chain (MRLC), myosin light chain kinase (MLCK), filamin, cortactin, p41Arc (a subunit of the Arp2/3 complex), caldesmon, paxillin and RhoGDI, to mention a few (Szczepanowska 2009).
Class II PAKs also have a CRIB domain, but lack a defined autoinhibitory domain and proline-rich regions. They do not require GTPases for their kinase activity, but their interaction with RAC or CDC42 affects their subcellular localization. Only conventional PAKs will be annotated here.
Protein kinases N (PKN), also known as protein kinase C-related kinases (PKR) feature a C-terminal serine/threonine kinase domain and three RHO-binding motifs at the N-terminus. RHO GTPases RHOA, RHOB, RHOC and RAC1 bind PKN1, PKN2 and PKN3 (Maesaki et al. 1999, Zhong et al. 1999, Owen et al. 2003, Modha et al. 2008, Hutchinson et al. 2011, Hutchinson et al. 2013), bringing them in proximity to the PIP3-activated co-activator PDPK1 (PDK1) (Flynn et al. 2000, Torbett et al. 2003). PDPK1 phosphorylates PKNs on a highly conserved threonine residue in the kinase activation loop, which is a prerequisite for PKN activation. Phosphorylation of other residues might also be involved in activation (Flynn et al. 2000, Torbett et al. 2003, Dettori et al. 2009). PKNs are activated by fatty acids like arachidonic acid and phospholipids in vitro, but the in vivo significance of this activation remains unclear (Palmer et al. 1995, Yoshinaga et al. 1999).
PKNs play important roles in diverse functions, including regulation of cell cycle, receptor trafficking, vesicle transport and apoptosis. PKN is also involved in the ligand-dependent transcriptional activation by the androgen receptor. More than 20 proteins and several peptides have been shown to be phosphorylated by PKN1 and PKN2, including CPI-17 (Hamaguchi et al. 2000), alpha-actinin (Mukai et al. 1997), adducin (Collazos et al. 2011), CDC25C (Misaki et al. 2001), vimentin (Matsuzawa et al. 1997), TRAF1 (Kato et al. 2008), CLIP170 (Collazos et al. 2011) and EGFR (Collazos et al. 2011). There are no known substrates for PKN3 (Collazos et al. 2011).
DNA synthesis occurs in the S phase, or the synthesis phase, of the cell cycle. The cell duplicates its hereditary material, and two copies of the chromosome are formed. As DNA replication continues, the E type cyclins shared by the G1 and S phases, are destroyed and the levels of the mitotic cyclins rise.
Semaphorins are a large family of cell surface and secreted guidance molecules divided into eight classes on the basis of their structures. They all have an N-terminal conserved sema domain. Semaphorins signal through multimeric receptor complexes that include other proteins such as plexins and neuropilins.
The epidermal growth factor receptor (EGFR) is one member of the ERBB family of transmembrane glycoprotein tyrosine receptor kinases (RTK). Binding of EGFR to its ligands induces conformational change that unmasks the dimerization interface in the extracellular domain of EGFR, leading to receptor homo- or heterodimerization at the cell surface. Dimerization of the extracellular regions of EGFR triggers additional conformational change of the cytoplasmic EGFR regions, enabling the kinase domains of two EGFR molecules to achieve the catalytically active conformation. Ligand activated EGFR dimers trans-autophosphorylate on tyrosine residues in the cytoplasmic tail of the receptor. Phosphorylated tyrosines serve as binding sites for the recruitment of signal transducers and activators of intracellular substrates, which then stimulate intracellular signal transduction cascades that are involved in regulating cellular proliferation, differentiation, and survival. Recruitment of complexes containing GRB2 and SOS1 to phosphorylated EGFR dimers either directly, through phosphotyrosine residues that serve as GRB2 docking sites, or indirectly, through SHC1 recruitment, promotes GDP to GTP exchange on RAS, resulting in the activation of RAF/MAP kinase cascade. Binding of complexes of GRB2 and GAB1 to phosphorylated EGFR dimers leads to formation of the active PI3K complex, conversion of PIP2 into PIP3, and activation of AKT signaling. Phospholipase C-gamma1 (PLCG1) can also be recruited directly, through EGFR phosphotyrosine residues that serve as PLCG1 docking sites, which leads to PLCG1 phosphorylation by EGFR and activation of DAG and IP3 signaling. EGFR signaling is downregulated by the action of ubiquitin ligase CBL. CBL binds directly to the phosphorylated EGFR dimer through the phosphotyrosine Y1045 in the C-tail of EGFR, and after CBL is phosphorylated by EGFR, it becomes active and ubiquitinates phosphorylated EGFR dimers, targeting them for degradation. For a recent review of EGFR signaling, please refer to Avraham and Yarden, 2011.
ERBB2, also known as HER2 or NEU, is a receptor tyrosine kinase (RTK) belonging to the EGFR family. ERBB2 possesses an extracellular domain that does not bind any known ligand, contrary to other EGFR family members, a single transmembrane domain, and an intracellular domain consisting of an active kinase and a C-tail with multiple tyrosine phosphorylation sites. Inactive ERBB2 is associated with a chaperone heat shock protein 90 (HSP90) and its co-chaperone CDC37 (Xu et al. 2001, Citri et al. 2004, Xu et al. 2005). In addition, ERBB2 is associated with ERBB2IP (also known as ERBIN or LAP2), a protein responsible for proper localization of ERBB2. In epithelial cells, ERBB2IP restricts expression of ERBB2 to basolateral plasma membrane regions (Borg et al. 2000).
ERBB2 becomes activated by forming a heterodimer with another ligand-activated EGFR family member, either EGFR, ERBB3 or ERBB4, which is accompanied by dissociation of chaperoning proteins HSP90 and CDC37 (Citri et al. 2004), as well as ERBB2IP (Borg et al. 2000) from ERBB2. ERBB2 heterodimers function to promote cell proliferation, cell survival and differentiation, depending on the cellular context. ERBB2 can also be activated by homodimerization when it is overexpressed, in cancer for example.
In cells expressing both ERBB2 and EGFR, EGF stimulation of EGFR leads to formation of both ERBB2:EGFR heterodimers (Wada et al. 1990, Karunagaran et al. 1996) and EGFR homodimers. Heterodimers of ERBB2 and EGFR trans-autophosphorylate on twelve tyrosine residues, six in the C-tail of EGFR and six in the C-tail of ERBB2 - Y1023, Y1139, Y1196, Y1221, Y1222 and Y1248 (Margolis et al. 1989, Hazan et al. 1990,Walton et al. 1990, Helin et al. 1991, Ricci et al. 1995, Pinkas-Kramarski 1996). Phosphorylated tyrosine residues in the C-tail of EGFR and ERBB2 serve as docking sites for downstream signaling molecules. Three key signaling pathways activated by ERBB2:EGFR heterodimers are RAF/MAP kinase cascade, PI3K-induced AKT signaling, and signaling by phospholipase C gamma (PLCG1). Downregulation of EGFR signaling is mediated by ubiquitin ligase CBL, and is shown under Signaling by EGFR.
In cells expressing ERBB2 and ERBB3, ERBB3 activated by neuregulin NRG1 or NRG2 binding (Tzahar et al. 1994) forms a heterodimer with ERBB2 (Pinkas-Kramarski et al. 1996, Citri et al. 2004). ERBB3 is the only EGFR family member with no kinase activity, and can only function in heterodimers, with ERBB2 being its preferred heterodimerization partner. After heterodimerization, ERBB2 phosphorylates ten tyrosine residues in the C-tail of ERBB3, Y1054, Y1197, Y1199, Y1222, Y1224, Y1260, Y1262, Y1276, Y1289 and Y1328 (Prigent et al. 1994, Pinkas-Kramarski et al. 1996, Vijapurkar et al. 2003, Li et al. 2007) that subsequently serve as docking sites for downstream signaling molecules, resulting in activation of PI3K-induced AKT signaling and RAF/MAP kinase cascade. Signaling by ERBB3 is downregulated by the action of RNF41 ubiquitin ligase, also known as NRDP1.
In cells expressing ERBB2 and ERBB4, ligand stimulated ERBB4 can either homodimerize or form heterodimers with ERBB2 (Li et al. 2007), resulting in trans-autophosphorylation of ERBB2 and ERBB4 on C-tail tyrosine residues that will subsequently serve as docking sites for downstream signaling molecules, leading to activation of RAF/MAP kinase cascade and, in the case of ERBB4 CYT1 isoforms, PI3K-induced AKT signaling (Hazan et al. 1990, Cohen et al. 1996, Li et al. 2007, Kaushansky et al. 2008). Signaling by ERBB4 is downregulated by the action of WWP1 and ITCH ubiquitin ligases, and is shown under Signaling by ERBB4.
As inferred from mouse, both non-phosphorylated and phosphorylated STAT3 can form dimers and enter the nucleus. Phosphorylation of STAT3 appears to change the equilibrium between these states, causing accumulation of phosphorylated STAT3 in the nucleus. Phosphorylated STAT3 dimers also activate transcription more efficiently.
As inferred from mouse, both non-phosphorylated and phosphorylated STAT3 are imported and exported from the nucleus. Phosphorylation shifts the equilibrium distribution of STAT3 to the nucleus.
Binding of PTK6 (BRK) to activated ERBB2 receptor stimulates autophosphorylation of PTK6 on tyrosine residue Y342 (Xiang et al. 2008, Peng et al. 2015). Autophosphorylation at Y342 significantly increases catalytic activity of PTK6 (Qiu and Miller 2002).
STAP2 binds to STAT3 and promotes STAT3 activation (Ikeda et al. 2009, Minoguchi et al. 2003). Phosphorylation of STAP2 at tyrosine residue Y250 (Minoguchi et al. 2003, Ikeda et al. 2009) and possibly also Y322 (Minoguchi et al. 2003) is needed for STAT3 binding. Phosphorylation of STAP2 by PTK6 at tyrosine Y250 enables STAP2 to simultaneously interact with PTK6 (BRK) and STAT3, thus recruiting STAT3 to PTK6 (Ikeda et al. 2009, Ikeda et al. 2010). The pleckstrin homology (PH) domain of STAP2 binds to PTK6, while the SH2 domain and the C-terminus of STAP2 interact with STAT3 (Ikeda et al. 2010).
STAP2 may promote nuclear translocation of PTK6, which could be dependent on STAT3 binding (Ikeda et al. 2010). STAP2 protein levels are negatively regulated by the E3 ubiquitin ligase CBL. CBL can form a complex with STAP2, but the direct ubiquitination of STAP2 by CBL has not been demonstrated (Sekine et al. 2009). PTK6, on the other hand, promotes CBL protein down-regulation (Kang and Lee 2013).
SOCS3, induced by activated STAT3, binds autophosphorylated PTK6 (BRK) and inhibits its catalytic activity and phosphorylation of STAT3, thus creating a negative feedback loop (Liu et al. 2006). The SH2 domain of SOCS3 binds to the kinase domain of autophosphorylated PTK6. Autophosphorylation of PTK6 on tyrosine residue Y251 (not shown) may be necessary for SOCS3 binding. Inhibition of the kinase activity of PTK6 requires the kinase inhibitory region (KIR) of SOCS3. SOCS3 may also modestly reduce PTK6 protein levels by recruiting ubiquitin ligases to PTK6, which requires the SOCS box of SOCS3 (Gao et al. 2012).
Activated PTK6 (BRK) phosphorylates STAT3 on tyrosine residue Y705. PTK6-mediated phosphorylation of STAT3 is promoted by STAP2 and inhibited by SOCS3 (Liu et al. 2006, Ikeda et al. 2010).
The promoter of the SOCS3 gene contains two STAT binding/response elements (SREs), in between the AP-1 site and the SP1/SP3 site. STAT3, the AP-1 (FOS:JUN) complex and SP1 or SP3 can all contribute to SOCS3 induction (Wiejak et al. 2012), which depends on the cellular context. In some cell types, binding of STAT3 may be necessary (Isobe et al. 2006) for stimulation of SOCS3 transcription. STAT1 but not STAT3 is important for SOCS3 induction downstream of interferon-gamma (IFNG) signaling (Gatto et al. 2004). STAT3 needs to be phosphorylated on tyrosine residue Y705 in order to bind the SOCS3 promoter and activate SOCS3 transcription (Yang et al. 2010).
Binding of STAT3 to STAT response elements (SREs) in the promoter of the SOCS3 gene stimulates SOCS3 transcription (Yang et al. 2010, Wiejak et al. 2012).
Activated PTK6 (BRK) binds to CDKN1B (p27KIP1) that is in a complex with CDK4 and cyclin D1 (CCND1). Since PTK6 increases cyclin E1 (CCNE1) levels downstream of ERBB2 while decreasing CDKN1B levels, PTK6 probably also associates with CDKN1B bound to the complex of CCNE1 and CDK2 (Xiang et al. 2008).
PTK6 (BRK) phosphorylates CDKN1B (p27KIP1) bound to the complex of CDK4 and CCND1 (cyclin D1) on tyrosine residue Y88 and possibly other tyrosines (e.g. Y89) (Patel et al. 2015). Based on the finding that PTK6 promotes ERBB2-induced increase in cyclin E1 (CCNE1) levels and decrease in CDKN1B levels (Xiang et al. 2008), and supported by the analogy with other SRC family kinases that phosphorylate CDKN1B (Grimmler et al. 2007), PTK6 is likely to also phosphorylate CDKN1B bound to the complex of CCNE1 and CDK2. Phosphorylation of CDKN1B (p27KIP1) on tyrosine residue Y88 by SRC family kinases dislodges the 3-10 helix of CDKN1B from the active site of CDK2 or CDK4, thus converting CDKN1B from a bound inhibitor to a bound non-inhibitor (Grimmler et al. 2007, Ray et al. 2009).
Activated PTK6 (BRK) phosphorylates PXN (paxillin) on tyrosine residues Y31 and Y118. PTK6-mediated phosphorylation of PXN can be triggered by EGF stimulation (Chen et al. 2004).
PXN (paxillin), phosphorylated by PTK6 (BRK) on tyrosine residues Y31 and Y118, recruits CRK (CrkII) complex which acts as a guanine exchange factor (GEF) for RAC1 (Chen et al. 2004).
PTK6 (BRK) mediated phosphorylation of PXN (paxillin), which may be triggered by EGF treatment, leads to formation of the RAC1 guanyl nucleotide exchange factor complex composed of PXN and the CRK (CrkII) complex, which includes DOCK180 and ELMO1 or ELMO2. Exchange of RAC1-bound GDP for GTP results in PTK6-induced RAC1 activation, which contributes to cell migration (Chen et al. 2004).
Activated PTK6 (BRK) phosphorylates BCAR1 (p130CAS) on tyrosine residues Y165 and Y664, and possibly other tyrosine residues. PTK6-mediated phosphorylation of BCAR1 contributes to formation of peripheral focal adhesion complexes involved in cell migration. Integrin receptors, growth factor receptors and ERK5 (MAPK7) contribute to PTK6-mediated formation of peripheral adhesion complexes (Zheng et al. 2012). PTK6-mediated phosphorylation of BCAR1 can also be triggered by UV-induced DNA damage and associated signaling (Chastkofsky et al. 2015).
Activated PTK6 (BRK) phosphorylates AKT1 on tyrosine residues Y315 and Y326. The SH2 domain of PTK6 binds phosphorylated tyrosines in AKT1, thus enhancing the interaction between PTK6 and AKT1. PTK6-mediated phosphorylation may facilitate subsequent activating phosphorylation of AKT1 in response to generation of PIP3 by PI3K (Zheng et al. 2010). In addition, binding of PTK6 to AKT1 may prevent AKT1 activity in unstimulated cells; however, this effect may be cell type specific (Zhang et al. 2005). EGF-stimulation causes the complex of PTK6 and AKT1 to dissociate, but the exact mechanism is not known (Zhang et al. 2005).
PTK6 (BRK) phosphorylates tumor suppressor DOK1 on tyrosine residue Y362. PTK6-mediated phosphorylation of DOK1 targets DOK1, through an unknown mechanism, for ubiquitin-dependent proteasome degradation (Miah et al. 2014).
Binding of HIF1A (HIF1-alpha) and/or EPAS1 (HIF2A) to hypoxia response elements (HREs) in the promoter region of the PTK6 (BRK) gene stimulates PTK6 transcription at hypoxia (Regan Anderson et al. 2013). EPAS1 was recently reported to cooperate with the activated glucocorticoid receptor NR3C1 (GCR) and its cofactor PELP1 in the stimulation of PTK6 transcription (Regan Anderson et al. 2016).
HIF1A (HIF1-alpha) and/or EPAS1 (HIF2A), probably in association with other transcription factors, binds hypoxia response elements (HREs) in the promoter region of the PTK6 (BRK) gene (Regan Anderson et al. 2013). EPAS1 was recently found to cooperate with the activated glucocorticoid receptor NR3C1 (GCR) and its cofactor PELP1 in binding to the adjacent hypoxia response and glucocorticoid response PTK6 promoter elements (Regan Anderson et al. 2016).
PTK6 (BRK) phosphorylates CBL at tyrosine residues Y700, Y731 and Y774, which are also targeted by other SRC family kinases. It has not been examined whether CBL and PTK6 interact directly. However, it has been shown that CBL expression is reciprocal (inversely related) to PTK6 in several cancer cell lines (Pires et al. 2014). CBL is an E3 ubiquitin ligase that negatively regulates EGFR, targeting it for degradation (Kang and Lee 2013). CBL is also implicated as a putative E3 ubiquitin ligase for PTK6 in normoxia (Pires et al. 2014).
ARAP1 is implicated in the endocytosis of EGFR, as the complex formation betwen ARAP1 and CIN85 inhibits CBL-mediated targeting of EGFR to the early endosome/lysosome pathway (Yoon et al. 2011). PTK6 phosphorylates ARAP1 on tyrosine residue Y231, resulting in the inhibition of EGFR endocytosis and, hence, prolonged EGFR signaling (Kang et al. 2010).
PTK6 (BRK) associates with the RNA binding protein KHDRBS1 (SAM68) in the nucleus, where PTK6 and KHDRBS1 colocalize in the SAM68-SLM nuclear bodies (SNBs) (Derry et al. 2000).
PTK6 phosphorylates KHDRBS1 (SAM68) on tyrosine residues Y435, Y440 and Y443, located within the nuclear localization signal (NLS) of KHDRBS1 (Lukong et al. 2005). PTK6-mediated phosphorylation inhibits the interaction of KHDRBS1 with RNA (Derry et al. 2000, Coyle et al. 2003).
PTK6 (BRK) mediated phosphorylation of nuclear localization signal (NLS) of the RNA binding protein KHDRBS1 (SAM68) results in nuclear exclusion of KHDRBS1 and interferes with the antiproliferative role of KHDRBS1 (Lukong et al. 2005).
Nuclear PTK6 (BRK) phosphorylates the RNA binding protein KHDRSB2 (SLM1) on an unknown tyrosine residue, thus inhibiting its interaction with RNA. KDRSB2 is a SAM68 (KHDRSB1) family member whose function has been poorly studied (Haegebarth et al. 2004).
Nuclear PTK6 (BRK) phosphorylates the RNA binding protein KHDRSB3 (SLM2) on an unknown tyrosine residue, thus inhibiting its interaction with RNA. KDRSB3 is a SAM68 (KHDRSB1) family member whose function has been poorly studied (Haegebarth et al. 2004).
ARHGAP35 (p190 Rho GTPase activating protein) binds GTP-bound RHOA (Li et al. 1997). Phosphorylation of ARHGAP35 by SRC family kinases (Holinstat et al. 2006), including PTK6 (Shen et al. 2008), is necessary for ARHGAP35-mediated activation of Rho GTPase activity. It is uncertain whether phosphorylation of ARHGAP35 by SRC family kinases is necessary for binding to RHOA.
Protein tyrosine kinase SRMS phosphorylates PTK6 (BRK) on a C-terminal tyrosine residue Y447, resulting in the inhibition of PTK6 kinase activity. In vitro, SRMS can phosphorylate PTK6 at Y447 in the absence of PTK6 autophosphorylation at Y342. It is not known if SRMS directly binds to PTK6 (Fan et al. 2015).
PTK6 (BRK) binds a large RNA processing nuclear complex that contains SFPQ (PSF) and phosphorylates SFPQ on C-terminal tyrosine residues. PTK6 also phosphorylates at least two additional SFPQ-associated unidentified proteins.
PTK6-mediated phosphorylation disrupts SFPQ binding to RNA and may promote the relocalization of SFPQ to the cytosol and cell cycle arrest (Lukong et al. 2009).
EPAS1 (HIF2A) and dexamethasone-activated glucocorticoid receptor NR3C1 (GCR or GR), in the presence of the NR3C1 co-factor PELP1, cooperatively bind to adjacent hypoxia response and glucocorticoid response elements in the PTK6 gene promoter. The cooperative binding of EPAS1 and NR3C1 to the PTK6 gene promoter may be facilitated by p38 MAPK-mediated phosphorylation of NR3C1 on serine residue S134. EPAS1 expression can also be stimulated by the activated NR3C1. EPAS1 and NR3C1-mediated activation of PTK6 expression may play an important role in the progression of the triple negative breast cancer (Regan Anderson et al. 2016).
EGFR bound to HBEGF (HB-EGF) can form heterodimers with the transmembrane glycoprotein GPNBM. The intracellular domain of GPNMB interacts with the kinase domain of EGFR (Lin et al. 2016).
HBEGF-bound EGFR phosphorylates its heterodimerization partner GPNMB at tyrosine residue Y525 (Lin et al. 2016). It is not clear whether trans-autophosphorylation of HBEGF-bound EGFR homodimers precedes heterodimerization of EGFR with GPNBM and GPNMB phosphorylation or if the interaction of GPNMB with the kinase domain of EGFR is sufficient for EGFR kinase activation.
Phosphorylation of GPNBM at tyrosine residue Y525 upon heterodimerization with HBEGF-bound EGFR promotes, in the presence of long non-coding RNA LINC011139 (LINK-A), the recruitment of PTK6 (BRK). In addition to PTK6, LINC01139 simultaneously recruits serine/threonine kinase LRRK2 to phosphorylated GPNBM (Lin et al. 2016).
The long non-coding RNA LINC01139 (LINK-A) induces conformational change of PTK6 (BRK), which facilitates PTK6 autophosphorylation on tyrosine residue Y351 and possibly other sites (Lin et al. 2016).
PTK6 (BRK) tyrosine kinase, activated via long non-coding RNA LINC01139 (LINK-A) mediated recruitment to phosphorylated GPNMB (bound to HBEGF-activated EGFR), phosphorylates hypoxia inducible factor 1 alpha (HIF1A) at tyrosine residue Y565. Phosphorylation of HIF1A by PTK6 at Y565 inhibits HIF1A hydroxylation at proline P564, resulting in HIF1A stabilization under normoxic conditions (Lin et al. 2016).
The human genome encodes at least 10 proteins that bind RAS and activate its intrinsic GTPase activity, resulting in the formation of inactive RAS:GDP and attenuating RAS signaling (reviewed in King et al, 2013). One of the identified RAS GAP proteins is RASA1, also known as p120 GAP. GAP proteins stimulate RAS GTPase activity by inserting a conserved arginine residue into the RAS active site, promoting a conformational change in the active site to allow GTP hydrolysis (Ahamdian et al, 2003; Scheffzek et al, 1997; Ahamdian et al, 1997). In addition to the GAP domain, most RAS GAP proteins also contain membrane targeting domains that facilitate interaction with the plasma membrane where RAS is tethered. In some cases, such as RASA3, membrane localization is constitutive, whereas in others, the GAP proteins are targeted to the membrane in response to cellular signaling. In addition to binding RAS, a number of GAP proteins also mediate other protein-protein interactions and act as scaffolds to integrate signaling; some GAPs are also known to bind and activate other small GTPases such as RAP (reviewed in King et al, 2013). Loss-of-functions mutations in RAS GAP proteins have been identified in a number of cancers (reviewed in Maertens and Cichowski, 2014).
LRRK2 serine/threonine kinase, activated via long non-coding RNA LINC01139 (LINK-A) mediated recruitment to phosphorylated GPNMB (bound to HBEGF-activated EGFR), phosphorylates hypoxia inducible factor 1 alpha (HIF1A) at serine residue S797. LRRK2-mediated phosphorylation of HIF1A at S797 promotes association of HIF1A with EP300 (p300) transcriptional co-activator and inhibits association of HIF1A with a transactivation inhibitor HIF1AN (FIH) (Lin et al. 2016).
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In the presence of oxygen members of the transcription factor family HIF-alpha, comprising HIF1A, HIF2A (EPAS1), and HIF3A, are hydroxylated on proline residues by PHD1 (EGLN2), PHD2 (EGLN1), and PHD3 (EGLN3) and on asparagine residues by HIF1AN (FIH) (reviewed in Pouyssegur et al. 2006, Semenza 2007, Kaelin and Ratcliffe 2008, Nizet and Johnson 2009, Brahimi-Horn and Pouyssegur 2009, Majmundar et al. 2010, Loenarz and Schofield 2011). Both types of reaction require molecular oxygen as a substrate and it is probable that at least some HIF-alpha molecules carry both hydroxylated asparagine and hydroxylated proline (Tian et al. 2011).
Hydroxylated asparagine interferes with the ability of HIF-alpha to interact with p300 and CBP while hydroxylated proline facilitates the interaction of HIF-alpha with the E3 ubiquitin ligase VHL, causing ubiquitination and proteolysis of HIF-alpha. Hypoxia inhibits both types of hydroxylation, resulting in the stabilization of HIF-alpha, which then enters the nucleus, binds HIF-beta, and recruits p300 and CBP to activate target genes such as EPO and VEGF.
During early G1, cells can enter a quiescent G0 state. In quiescent cells, the evolutionarily conserved DREAM complex, consisting of the pocket protein family member p130 (RBL2), bound to E2F4 or E2F5, and the MuvB complex, represses transcription of cell cycle genes (reviewed by Sadasivam and DeCaprio 2013).
During early G1 phase in actively cycling cells, transcription of cell cycle genes is repressed by another pocket protein family member, p107 (RBL1), which forms a complex with E2F4 (Ferreira et al. 1998, Cobrinik 2005). RB1 tumor suppressor, the product of the retinoblastoma susceptibility gene, is the third member of the pocket protein family. RB1 binds to E2F transcription factors E2F1, E2F2 and E2F3 and inhibits their transcriptional activity, resulting in prevention of G1/S transition (Chellappan et al. 1991, Bagchi et al. 1991, Chittenden et al. 1991, Lees et al. 1993, Hiebert 1993, Wu et al. 2001). Once RB1 is phosphorylated on serine residue S795 by Cyclin D:CDK4/6 complexes, it can no longer associate with and inhibit E2F1-3. Thus, CDK4/6-mediated phosphorylation of RB1 leads to transcriptional activation of E2F1-3 target genes needed for the S phase of the cell cycle (Connell-Crowley et al. 1997). CDK2, in complex with cyclin E, contributes to RB1 inactivation and also activates proteins needed for the initiation of DNA replication (Zhang 2007). Expression of D type cyclins is regulated by extracellular mitogens (Cheng et al. 1998, Depoortere et al. 1998). Catalytic activities of CDK4/6 and CDK2 are controlled by CDK inhibitors of the INK4 family (Serrano et al. 1993, Hannon and Beach 1994, Guan et al. 1994, Guan et al. 1996, Parry et al. 1995) and the Cip/Kip family, respectively.
The importance of the RAS/RAF MAPK cascade is highlighted by the fact that components of this pathway are mutated with high frequency in a large number of human cancers. Activating mutations in RAS are found in approximately one third of human cancers, while ~8% of tumors express an activated form of BRAF (Roberts and Der, 2007; Davies et al, 2002; Cantwell-Dorris et al, 2011).
DRFs activated by RHO GTPases contain a GTPase binding domain (GBD) at their N-terminus, followed by formin homology domains 3, 1, and 2 (FH3, FH1, FH2) and a diaphanous autoregulatory domain (DAD) at the C-terminus. Most DRFs contain a dimerization domain (DD) and a coiled-coil region (CC) in between FH3 and FH1 domains (reviewed by Kuhn and Geyer 2014). RHO GTPase-activated DRFs are autoinhibited through the interaction between FH3 and DAD which is disrupted upon binding to an active RHO GTPase (Li and Higgs 2003, Lammers et al. 2005, Nezami et al. 2006). Since formins dimerize, it is not clear whether the FH3-DAD interaction is intra- or intermolecular. FH2 domain is responsible for binding to the F-actin and contributes to the formation of head-to-tail formin dimers (Xu et al. 2004). The proline-rich FH1 domain interacts with the actin-binding proteins profilins, thereby facilitating actin recruitment to formins and accelerating actin polymerization (Romero et al. 2004, Kovar et al. 2006).
Different formins are activated by different RHO GTPases in different cell contexts. FMNL1 (formin-like protein 1) is activated by binding to the RAC1:GTP and is involved in the formation of lamellipodia in macrophages (Yayoshi-Yamamoto et al. 2000) and is involved in the regulation of the Golgi complex structure (Colon-Franco et al. 2011). Activation of FMNL1 by CDC42:GTP contributes to the formation of the phagocytic cup (Seth et al. 2006). Activation of FMNL2 (formin-like protein 2) and FMNL3 (formin-like protein 3) by RHOC:GTP is involved in cancer cell motility and invasiveness (Kitzing et al. 2010, Vega et al. 2011). DIAPH1, activated by RHOA:GTP, promotes elongation of actin filaments and activation of SRF-mediated transcription which is inhibited by unpolymerized actin (Miralles et al. 2003). RHOF-mediated activation of DIAPH1 is implicated in formation of stress fibers (Fan et al. 2010). Activation of DIAPH1 and DIAPH3 by RHOB:GTP leads to actin coat formation around endosomes and regulates endosome motility and trafficking (Fernandez-Borja et al. 2005, Wallar et al. 2007). Endosome trafficking is also regulated by DIAPH2 transcription isoform 3 (DIAPH2-3) which, upon activation by RHOD:GTP, recruits SRC kinase to endosomes (Tominaga et al. 2000, Gasman et al. 2003). DIAPH2 transcription isoform 2 (DIAPH2-2) is involved in mitosis where, upon being activated by CDC42:GTP, it facilitates the capture of astral microtubules by kinetochores (Yasuda et al. 2004, Cheng et al. 2011). DIAPH2 is implicated in ovarian maintenance and premature ovarian failure (Bione et al. 1998). DAAM1, activated by RHOA:GTP, is involved in linking WNT signaling to cytoskeleton reorganization (Habas et al. 2001).
While the binding of CIT to RHO GTPases RHOA, RHOB, RHOC and RAC1 is well established (Madaule et al. 1995), the mechanism of CIT activation by GTP-bound RHO GTPases has not been elucidated. There are indications that CIT may be activated through autophosphorylation in the presence of active forms of RHO GTPases (Di Cunto et al. 1998). CIT appears to phosphorylate the myosin regulatory light chain (MRLC), the only substrate identified to date, on the same residues that are phosphorylated by ROCKs, but it has not been established yet how this relates to activation by RHO GTPases (Yamashiro et al. 2003). CIT and RHOA are implicated to act together in Golgi apparatus organization through regulation of the actin cytoskeleton (Camera et al. 2003). CIT is also involved in the regulation of cytokinesis through its interaction with KIF14 (Gruneberg et al. 2006, Bassi et al. 2013, Watanabe et al. 2013) and p27(Kip1) (Serres et al. 2012).
IQGAP1 is involved in the regulation of adherens junctions through its interaction with E-cadherin (CDH1) and catenins (CTTNB1 and CTTNA1) (Kuroda et al. 1998, Hage et al. 2009). IQGAP1 contributes to cell polarity and lamellipodia formation through its interaction with microtubules (Fukata et al. 2002, Suzuki and Takahashi 2008).
PAK1, PAK2 and PAK3 are direct effectors of RAC1 and CDC42 GTPases. RAC1 and CDC42 bind to the CRIB domain. This binding induces a conformational change that disrupts inactive PAK homodimers and relieves autoinhibition of the catalytic carboxyl terminal domain (Manser et al. 1994, Manser et al. 1995, Zhang et al. 1998, Lei et al. 2000, Parrini et al. 2002; reviewed by Daniels and Bokoch 1999, Szczepanowska 2009). Autophosphorylation of a conserved threonine residue in the catalytic domain of PAKs (T423 in PAK1, T402 in PAK2 and T436 in PAK3) is necessary for the kinase activity of PAK1, PAK2 and PAK3. Autophosphorylation of PAK1 serine residue S144, PAK2 serine residue S141, and PAK3 serine residue S154 disrupts association of PAKs with RAC1 or CDC42 and enhances kinase activity (Lei et al. 2000, Chong et al. 2001, Parrini et al. 2002, Jung and Traugh 2005, Wang et al. 2011). LIMK1 is one of the downstream targets of PAK1 and is activated through PAK1-mediated phosphorylation of the threonine residue T508 within its activation loop (Edwards et al. 1999). Further targets are the myosin regulatory light chain (MRLC), myosin light chain kinase (MLCK), filamin, cortactin, p41Arc (a subunit of the Arp2/3 complex), caldesmon, paxillin and RhoGDI, to mention a few (Szczepanowska 2009).
Class II PAKs also have a CRIB domain, but lack a defined autoinhibitory domain and proline-rich regions. They do not require GTPases for their kinase activity, but their interaction with RAC or CDC42 affects their subcellular localization. Only conventional PAKs will be annotated here.
PKNs play important roles in diverse functions, including regulation of cell cycle, receptor trafficking, vesicle transport and apoptosis. PKN is also involved in the ligand-dependent transcriptional activation by the androgen receptor. More than 20 proteins and several peptides have been shown to be phosphorylated by PKN1 and PKN2, including CPI-17 (Hamaguchi et al. 2000), alpha-actinin (Mukai et al. 1997), adducin (Collazos et al. 2011), CDC25C (Misaki et al. 2001), vimentin (Matsuzawa et al. 1997), TRAF1 (Kato et al. 2008), CLIP170 (Collazos et al. 2011) and EGFR (Collazos et al. 2011). There are no known substrates for PKN3 (Collazos et al. 2011).
ERBB2 becomes activated by forming a heterodimer with another ligand-activated EGFR family member, either EGFR, ERBB3 or ERBB4, which is accompanied by dissociation of chaperoning proteins HSP90 and CDC37 (Citri et al. 2004), as well as ERBB2IP (Borg et al. 2000) from ERBB2. ERBB2 heterodimers function to promote cell proliferation, cell survival and differentiation, depending on the cellular context. ERBB2 can also be activated by homodimerization when it is overexpressed, in cancer for example.
In cells expressing ERBB2 and ERBB4, ligand stimulated ERBB4 can either homodimerize or form heterodimers with ERBB2 (Li et al. 2007), resulting in trans-autophosphorylation of ERBB2 and ERBB4 on C-tail tyrosine residues that will subsequently serve as docking sites for downstream signaling molecules, leading to activation of RAF/MAP kinase cascade and, in the case of ERBB4 CYT1 isoforms, PI3K-induced AKT signaling (Hazan et al. 1990, Cohen et al. 1996, Li et al. 2007, Kaushansky et al. 2008). Signaling by ERBB4 is downregulated by the action of WWP1 and ITCH ubiquitin ligases, and is shown under Signaling by ERBB4.In cells expressing both ERBB2 and EGFR, EGF stimulation of EGFR leads to formation of both ERBB2:EGFR heterodimers (Wada et al. 1990, Karunagaran et al. 1996) and EGFR homodimers. Heterodimers of ERBB2 and EGFR trans-autophosphorylate on twelve tyrosine residues, six in the C-tail of EGFR and six in the C-tail of ERBB2 - Y1023, Y1139, Y1196, Y1221, Y1222 and Y1248 (Margolis et al. 1989, Hazan et al. 1990,Walton et al. 1990, Helin et al. 1991, Ricci et al. 1995, Pinkas-Kramarski 1996). Phosphorylated tyrosine residues in the C-tail of EGFR and ERBB2 serve as docking sites for downstream signaling molecules. Three key signaling pathways activated by ERBB2:EGFR heterodimers are RAF/MAP kinase cascade, PI3K-induced AKT signaling, and signaling by phospholipase C gamma (PLCG1). Downregulation of EGFR signaling is mediated by ubiquitin ligase CBL, and is shown under Signaling by EGFR.
In cells expressing ERBB2 and ERBB3, ERBB3 activated by neuregulin NRG1 or NRG2 binding (Tzahar et al. 1994) forms a heterodimer with ERBB2 (Pinkas-Kramarski et al. 1996, Citri et al. 2004). ERBB3 is the only EGFR family member with no kinase activity, and can only function in heterodimers, with ERBB2 being its preferred heterodimerization partner. After heterodimerization, ERBB2 phosphorylates ten tyrosine residues in the C-tail of ERBB3, Y1054, Y1197, Y1199, Y1222, Y1224, Y1260, Y1262, Y1276, Y1289 and Y1328 (Prigent et al. 1994, Pinkas-Kramarski et al. 1996, Vijapurkar et al. 2003, Li et al. 2007) that subsequently serve as docking sites for downstream signaling molecules, resulting in activation of PI3K-induced AKT signaling and RAF/MAP kinase cascade. Signaling by ERBB3 is downregulated by the action of RNF41 ubiquitin ligase, also known as NRDP1.
Annotated Interactions
STAP2 may promote nuclear translocation of PTK6, which could be dependent on STAT3 binding (Ikeda et al. 2010). STAP2 protein levels are negatively regulated by the E3 ubiquitin ligase CBL. CBL can form a complex with STAP2, but the direct ubiquitination of STAP2 by CBL has not been demonstrated (Sekine et al. 2009). PTK6, on the other hand, promotes CBL protein down-regulation (Kang and Lee 2013).
PTK6-mediated phosphorylation disrupts SFPQ binding to RNA and may promote the relocalization of SFPQ to the cytosol and cell cycle arrest (Lukong et al. 2009).